How can I manage multiple animations in one .blend file?
If you go to the Dopesheet View you can create and name separate animations with the Action Editor pane. You can also use the main Dopesheet pane to scale your animations.



Each of these animations as it relates to the objects do have their own separate timelines within Blender and can be linked or copied to other .blend files.

Also you can press M in the timeline to add a marker. I would really recommend desisting from the approach you have been using as it's very inefficient and is prone to error.